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In no particular order, from games I've played:

• Anodyne - Think Gameboy Zelda with a strong eldritch vibe.
• Bastion - I know people already mentioned this but it stands repeating. Gameplay's solid, music's great, and story's cool.
• CrossCode - I don't care the game's not fully out yet. Old school Square or Enix action-adventure games meets puzzles and Mega Man style bullets that bounce off of certain surfaces. Get this. There's a really good demo that's practically a game of its own. Play that first. Then get the game.
• Dungeons of Dredmor - Where to begin? Unique roguelike with easy modability, good graphics, and weird but fun.
• Evoland - Original Version- Maybe not your cup of tea but I like it. Basically warps over time from a Zelda-like into Final Fantasy 8. Yes, this includes the card game.
• Freedom Planet - Remember Genesis-era Sonic? Did you love Genesis-era Sonic? So did the devs.
• Megabyte Punch - Custom robot beatemup. What's not to love? Seriously: get this.
• Momodora III - This is really great. It's kind of similar to Cave Story if you squint but it is so far the latest of a freeware series that happens to have a price tag. I really recommend playing the first two as a sort of demo.
• [Recettear, Chantelise, and Fortune Summoners (Bundle Link)- Okay, the reason why I list all three is that two are by one dev and the third are included in the translation company's Steam bundle. Between shop running with a barter system, top-down action-adventure dungeons, and sidescrolling metroidvania-style action, it's kind of hard to pick between which I want to recommend more.
• Super Chibi Knight - The original is a free browser game "Chibi Knight". Basically, think Zelda 2. Only big thing I can think of right now is the fact that the dev's daughter did a lot of sounds for it.

Honorable Mentions:
1000 Amps, Before the Echo, Demolition Inc, FRACT OSC, Glitchspace [Hexcells, Hexcells Plus, Hexcells Infinite (Bundle Link), Ossuary (has demo), Secrets of Rætikon, Shipwreck, The Wonderful End of the World (has demo).

Honorable (played as demo) Mentions:
Desktop Dungeons (Finished version ), Magicmaker, Paper Dungeons, The Talos Principle with Sigils of Elohim as a free side puzzle game.

Let's see...

1) Unepic
2) Nihilumbra
3) To the Moon
4) Terraria
5) Gunpoint
6) About Love, Hate & the other ones
7) Amnesia
8) Evil Quest
9) Metal Dead
10) Binding of Isaac

Miasmata
Knytt underground
The swapper
Gone home
Guacamelee
Papo & yo
The binding of isaac
Braid
Naissancee
Penumbra overture

Mark of the Ninja is for me.

EVOLAND
EVOLAND
EVOLAND
EVOLAND
EVOLAND
EVOLAND
EVOLAND
EVOLAND
EVOLAND

i'll just add Defense Grid, the rest have already been mentioned.

specially braid :3

depends how indie you are going..

The Long Dark
Stranded Deep
The Forest

i mean how many copies sell before they turn from indie to non-indie?

In no particular order:
Rogue Legacy
Bastion
Super Meat Boy
Castle Crashers
FTL Faster Than Light
Spelunky
Torchlight 2
Guacamelee
Desktop Dungeons
Transistor
Mark of the Ninja
Outland
Risk of Rain
Darkest Dungeon
Skullgirls
Towerfall Ascension
Unepic

I spent way longer than I should have trying to shorten it to ten. I might come back and edit this post into a top ten and have the others be honorable mentions, but it's unlikely XD